Move Uberon-related search tests under the providers package

Author: arteymix

test/ubic/basecode/ontology/providers/UberonOntologySearchTest.java

@@ -0,0 +1,54 @@
+package ubic.basecode.ontology.providers;
+
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntModel;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import ubic.basecode.ontology.jena.OntologyLoader;
+import ubic.basecode.ontology.jena.search.OntologyIndexer;
+import ubic.basecode.ontology.jena.search.OntologySearch;
+import ubic.basecode.ontology.jena.search.SearchIndex;
+import ubic.basecode.ontology.search.OntologySearchException;
+import ubic.basecode.ontology.search.OntologySearchTest;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.zip.GZIPInputStream;
+
+import static java.util.Objects.requireNonNull;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+public class UberonOntologySearchTest {
+    private static OntModel uberon;
+    private static SearchIndex uberonIndex;
+
+    @BeforeClass
+    public static void setUpUberon() throws IOException {
+        try ( InputStream is = new GZIPInputStream( requireNonNull( OntologySearchTest.class.getResourceAsStream( "/data/uberon.owl.gz" ) ) ) ) {
+            uberon = OntologyLoader.loadMemoryModel( is, "UBERON_TEST2" );
+            uberonIndex = OntologyIndexer.indexOntology( "UBERON_TEST2", uberon, false );
+        }
+    }
+
+    @Test
+    public void testOmitDefinition() throws OntologySearchException {
+        OntClass brain = uberon.getOntClass( "http://purl.obolibrary.org/obo/UBERON_0000955" );
+        assertNotNull( brain );
+        Set<OntologySearch.SearchResult<OntClass>> searchResults = OntologySearch.matchClasses( uberon, uberonIndex, "brain" ).toSet();
+        assertEquals( 128, searchResults.size() );
+    }
+
+    @Test
+    public void testScore() throws OntologySearchException {
+        OntClass brain = uberon.getOntClass( "http://purl.obolibrary.org/obo/UBERON_0000955" );
+        assertNotNull( brain );
+        List<OntologySearch.SearchResult<OntClass>> searchResults = OntologySearch.matchClasses( uberon, uberonIndex, "brain" ).toList();
+        assertEquals( 446, searchResults.size() );
+        assertEquals( 3.33, searchResults.get( 0 ).score, 0.01 );
+        assertEquals( 128, new HashSet<>( searchResults ).size() );
+    }
+}

…ntology/providers/UberonServiceTest.java …providers/UberonOntologyServiceTest.javatest/ubic/basecode/ontology/providers/UberonServiceTest.java renamed to test/ubic/basecode/ontology/providers/UberonOntologyServiceTest.java test/ubic/basecode/ontology/providers/UberonServiceTest.java renamed to test/ubic/basecode/ontology/providers/UberonOntologyServiceTest.java

@@ -16,9 +16,8 @@
 
 import static java.util.Objects.requireNonNull;
 import static org.junit.Assert.*;
-import static org.junit.Assert.assertTrue;
 
-public class UberonServiceTest extends AbstractOntologyTest {
+public class UberonOntologyServiceTest extends AbstractOntologyTest {
 
     private static OntologyService uberon;
 

test/ubic/basecode/ontology/search/OntologySearchTest.java

@@ -17,19 +17,17 @@
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.shared.JenaException;
-import org.junit.BeforeClass;
 import org.junit.Test;
 import ubic.basecode.ontology.AbstractOntologyTest;
 import ubic.basecode.ontology.jena.OntologyLoader;
 import ubic.basecode.ontology.jena.OntologyTermImpl;
-import ubic.basecode.ontology.jena.search.*;
+import ubic.basecode.ontology.jena.search.OntologyIndexer;
 import ubic.basecode.ontology.jena.search.OntologySearch;
+import ubic.basecode.ontology.jena.search.OntologySearchJenaException;
+import ubic.basecode.ontology.jena.search.SearchIndex;
 
-import java.io.IOException;
 import java.io.InputStream;
 import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
 import java.util.Set;
 import java.util.zip.GZIPInputStream;
 
@@ -45,17 +43,6 @@
  */
 public class OntologySearchTest extends AbstractOntologyTest {
 
-    private static OntModel uberon;
-    private static SearchIndex uberonIndex;
-
-    @BeforeClass
-    public static void setUpUberon() throws IOException {
-        try ( InputStream is = new GZIPInputStream( requireNonNull( OntologySearchTest.class.getResourceAsStream( "/data/uberon.owl.gz" ) ) ) ) {
-            uberon = OntologyLoader.loadMemoryModel( is, "UBERON_TEST2" );
-            uberonIndex = OntologyIndexer.indexOntology( "UBERON_TEST2", uberon, false );
-        }
-    }
-
     @Test
     public final void testIndexing() throws Exception {
         InputStream is = new GZIPInputStream( requireNonNull( this.getClass().getResourceAsStream( "/data/mged.owl.gz" ) ) );
@@ -246,23 +233,6 @@ public final void testOmitDefinitions4() throws Exception {
         index.close();
     }
 
-    @Test
-    public void testOmitDefinition() throws OntologySearchException {
-        OntClass brain = uberon.getOntClass( "http://purl.obolibrary.org/obo/UBERON_0000955" );
-        assertNotNull( brain );
-        Set<OntologySearch.SearchResult<OntClass>> searchResults = OntologySearch.matchClasses( uberon, uberonIndex, "brain" ).toSet();
-        assertEquals( 128, searchResults.size() );
-    }
-
-    @Test
-    public void testScore() throws OntologySearchException {
-        OntClass brain = uberon.getOntClass( "http://purl.obolibrary.org/obo/UBERON_0000955" );
-        assertNotNull( brain );
-        List<OntologySearch.SearchResult<OntClass>> searchResults = OntologySearch.matchClasses( uberon, uberonIndex, "brain" ).toList();
-        assertEquals( 446, searchResults.size() );
-        assertEquals( 3.334063, searchResults.get( 0 ).score, 0.000001 );
-        assertEquals( 128, new HashSet<>( searchResults ).size() );
-    }
 
     @Test
     public final void testPersistence() throws Exception {